1. Field of the Invention
The present invention relates generally to the fields of protein biology and oncology. More particularly, it concerns the classification of skin lesions based on mass spectrometry analysis of proteins from the lesions.
2. Description of Related Art
Ever since the first description of Spitz nevus (SN) by Sophie Spitz in 1948, pathologists and dermatopathologists in particular have been struggling with the distinction between SN and Spitzoid malignant melanoma (SMM). To diagnose a young child with melanoma, which has devastating consequences, and subject the child to surgery and chemotherapy is not a simple matter.
Spitzoid neoplasms are melanocytic lesions that include a spectrum ranging from completely benign “typical” SN to malignant melanomas that show “Spitzoid” features-SMM. The gold standard for diagnosing SN and differentiating it from SMM is histopathologic examination applying well established criteria. However, there are melanocytic lesions, which show conflicting histopathologic criteria and the distinction between a benign SN and SMM may be extremely difficult. These lesions are referred to as “atypical SN” or “atypical Spitzoid tumors/neoplasms.” (Binder, et al. 1993; Barnhill, et al. 1995; Crotty, et al. 2002 and Ferrara, et al. 2005). There is a great interobserver variability and discordance even among expert dermatopathologists regarding Spitzoid neoplasms. (Barnhill, et al. 1995; Ackerman 1996; Barnhill, et al. 1999; Farmer, et al. 1996 and Rapini 1999). The presence of a gray area, in which it is extremely difficult or utterly impossible to distinguish between SN and SMM, continues to present a weak point in clinical diagnosis of these two closely related diseases.
Ancillary techniques such as comparative genomic hybridization and fluorescent in situ hybridization may be helpful. The majority of SN reveal no DNA copy number changes by comparative genomic hybridization. (Bastian, et al. 1999; Bastian, et al. 2003; Harvell, et al. 2004). Approximately 20% of SN show an isolated gain of chromosome 11p. (Bastian, et al. 1999). A subset of SN with 11p copy number increases has H-RAS mutation; however, that is extremely uncommon in cutaneous melanoma. (Bastian, 2000 and van Engen-van Grunsven, et al. 2010). In contrast, more than 95% of conventional melanomas show multiple chromosomal aberrations including gains and loses by comparative genomic hybridization. (Bastian, et al. 1998 and Curtin, et al. 2005).
B-RAF mutations have been found only in a small subset of SN, whereas the majority of conventional melanomas have B-RAF or N-RAS mutations. (Fullen, et al. 2006) Furthermore, activating hot spot mutations in the B-RAF, N-RAS, and H-RAS genes were not identified in SMM or SN (Lee, et al. 2006 and Gill, et al. 2004). These data suggest that SMM might be a distinct form of melanoma with unknown genes and/or signaling pathways involved in its development (Lee, et al. 2006; Gaiser, et al. 2010 and Raskin, et al. 2011).
Matrix-assisted laser desorption ionization (MALDI) imaging mass spectrometry (IMS) is a powerful method for analyzing metabolites, peptides and proteins, DNA segments, and lipids directly from tissue sections with spatial fidelity. Although gene expression is useful for distinguishing melanocytic nevi from melanomas, it does not always correlate with protein translation and does not account for posttranslational modification (PTM). However, both protein expression level and PTM state have fundamental effect on cellular function or dysfunction; therefore, it is more meaningful to analyze proteins and peptides that are involved in the development and progression of diseases, especially cancer. IMS has the ability to discover molecular signatures of diseases and cancer. These molecular signatures are typically comprised of 5-20 different proteins that together result in robust diagnostic patterns (Caprioli and Farmer, 1997 and Zimmerman, et al. 2008). IMS-based studies have been used to elucidate molecular signatures of different tumor types and grades including brain, oral, lung, breast, gastric, pancreatic, renal, ovarian and prostate cancers (Groseclose, et al. 2008; Nathan, et al. 2002; Oppenheimer, et al. 2010 and Yanagisawa, et al. 2003).